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I think this setting is saved in one of the preference files for the browser. Using a snapshotting tool, change this setting and see if one of the .js files on the machine changes. For the version of Firefox I have installed here (11.0) I think it's in the file C:\Program Files\Mozilla Firefox\greprefs.js, but I think this was different for older versions.

Anyway, once you've identified the correct file, you could modify these settings through scripting.

Thanks for the feedback PJ, but it's actually not what I'm after here.
I need a "fix" which enables Java for Mozilla family browsers. See the print screen above. I want the checkbox to be checked and I can't for my life figure out how to. =(
Edit: The original package installation was done not to enable support for Mozilla.

I tried the deployment.properties hack also, but was unsuccesful.
However, I was changing the file located in the user profile, but I guess I need to change a global deployment.properties file. I can't find any though. =/
I was hoping for a -Xusage command, but no.

a system-wide deployment.properties file goes into C:\Windows\Sun\Java\Deployment\deployment.config or $Java Home$\lib\deployment.config
It's entirely possible it's not there and you need to put it there yourself. If the hack does not work for the file in the user profile though, I'm not sure if it will work at all...

That didn't really help me Piyush.
I've already managed to package Firefox, that's not the issue here. The issue is purely Java related and how to enable checkbox for the Mozilla family in the console.